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https://github.com/metaphorme/autodock-vina-docker

Package AutoDock Vina, ADFR suite, Meeko, MGLTools into Docker Image.
https://github.com/metaphorme/autodock-vina-docker

autodock autodock-vina autodocktools

Last synced: 4 months ago
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Package AutoDock Vina, ADFR suite, Meeko, MGLTools into Docker Image.

Awesome Lists containing this project

README 

          
# AutoDock-Vina-Docker



[![AutoDock Release](https://github.com/Metaphorme/AutoDock-Vina-Docker/actions/workflows/build_autodock_release.yml/badge.svg)](https://github.com/Metaphorme/AutoDock-Vina-Docker/actions/workflows/build_autodock_release.yml)

[![AutoDock Develop](https://github.com/Metaphorme/AutoDock-Vina-Docker/actions/workflows/build_autodock_develop.yml/badge.svg)](https://github.com/Metaphorme/AutoDock-Vina-Docker/actions/workflows/build_autodock_develop.yml)

[![MGLTools Image](https://github.com/Metaphorme/AutoDock-Vina-Docker/actions/workflows/build_mgltools.yml/badge.svg)](https://github.com/Metaphorme/AutoDock-Vina-Docker/actions/workflows/build_mgltools.yml)

![License](https://img.shields.io/github/license/Metaphorme/AutoDock-Vina-Docker?logo=opensourceinitiative)



Package [AutoDock Vina](https://github.com/ccsb-scripps/AutoDock-Vina), [ADFR suite](https://ccsb.scripps.edu/adfr/), [Meeko](https://github.com/forlilab/Meeko), [MGLTools](https://ccsb.scripps.edu/mgltools/) into Docker image.



**Notice:** Please makesure you will obey the License of [AutoDock Vina](https://autodock-vina.readthedocs.io/en/latest/citations.html), [ADFR software suite Non-Commercial Use](https://ccsb.scripps.edu/adfr/license/), [Meeko](https://github.com/forlilab/Meeko/blob/develop/LICENSE) before downloading this Docker image.



## Introduction



We provide [vina](https://github.com/users/Metaphorme/packages/container/package/vina), [vina-python](https://github.com/users/Metaphorme/packages/container/package/vina-python), [vina-all](https://github.com/users/Metaphorme/packages/container/package/vina-all) package for you to choose. Please refer to the table below to compare the differences.



| Package                                                      | Included programs                                            | Arch        |

| :----------------------------------------------------------- | ------------------------------------------------------------ | ----------- |

| [vina](https://github.com/users/Metaphorme/packages/container/package/vina) | vina binary, vice versa                                      | amd64/arm64 |

| [vina-python](https://github.com/users/Metaphorme/packages/container/package/vina-python) | vina binary, vice versa, vina python bindings, Meeko         | amd64/arm64 |

| [vina-all](https://github.com/users/Metaphorme/packages/container/package/vina-all) | vina binary, vice versa, vina python bindings, Meeko, ADFR Suite | amd64       |

| [AutoDockTools (MGLTools)](https://github.com/users/Metaphorme/packages/container/package/mgltools) | MGLTools                                                     | amd64       |



Because of the lack arm64 support of **ADFR Suite** and **MGLTools**, we can't provide arm64 images with ADFR Suite and MGLTools.



## Get Docker Image



**⚠️Warning: The `release` tag is deprecated, use a specific tag for a specific release version instead.**



### From Github



```bash

# vina



# Build from certain version like "v1.2.5"

# To check full version supported, please click https://github.com/Metaphorme/AutoDock-Vina-Docker/pkgs/container/vina

docker pull ghcr.io/metaphorme/vina:v1.2.5



# Build from https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop

docker pull ghcr.io/metaphorme/vina:develop



# vina-python



# Build from certain version like "v1.2.5"

# To check full version supported, please click https://github.com/Metaphorme/AutoDock-Vina-Docker/pkgs/container/vina-python

docker pull ghcr.io/metaphorme/vina-python:v1.2.5



# Build from https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop

docker pull ghcr.io/metaphorme/vina-python:develop



# vina-all



# Build from certain version like "v1.2.5"

# To check full version supported, please click https://github.com/Metaphorme/AutoDock-Vina-Docker/pkgs/container/vina-all

docker pull ghcr.io/metaphorme/vina-all:v1.2.5



# Build from https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop

docker pull ghcr.io/metaphorme/vina-all:develop



# MGLTools

docker pull ghcr.io/metaphorme/mgltools

```



### Build in local



```bash

git clone https://github.com/Metaphorme/AutoDock-Vina-Docker.git

cd AutoDock-Vina-Docker

# To build Dockerfile-vina* image

TAG_NAME=v1.2.5

docker build --build-arg BRANCHES=$TAG_NAME -t $TAG_NAME - < Dockerfile-vina-[name]

# To build MGLTools image

docker build -t mgltools - < Dockerfile-mgltools

```



## Run Docker Image



## vina



* Exec commands and mount $PWD to /data



  ```bash

  docker run -v $PWD:/data --rm ghcr.io/metaphorme/vina:v1.2.5 \

        vina --ligand 1iep_ligand.pdbqt --maps 1iep_receptor --scoring ad4 \

             --exhaustiveness 32 --out 1iep_ligand_ad4_out.pdbqt

  ```



​		**Notice:** `$PWD` means the current working directory; `/data` is contained in $PATH.



## vina-python



* Enter the shell and mount $PWD to /data



  ```bash

  docker run -it -v $PWD:/data --rm ghcr.io/metaphorme/vina-python:v1.2.5

  ```



  **Notice:** `$PWD` means the current working directory; `/data` is contained in $PATH.



* Commands (For example)



  ```bash

  # AutoDock Vina

  vina

  # AutoDock Vina Python bindings

  mk_prepare_ligand.py

  ```



* Software Locations



  ```bash

  # AutoDock Vina

  /opt/AutoDock-Vina

  # miniconda

  /opt/conda

  ```



## vina-all



* Enter the shell and mount $PWD to /data



  ```bash

  docker run -it -v $PWD:/data --rm ghcr.io/metaphorme/vina-all:v1.2.5

  ```



	**Notice:** `$PWD` means the current working directory.



* Commands (For example)



  ```bash

  # AutoDock Vina

  vina

  # AutoDock Vina Python bindings

  mk_prepare_ligand.py

  # ADFR Suite

  prepare_receptor

  autogrid4

  # Python2

  pythonsh

  ```



* Software Locations



  ```bash

  # AutoDock Vina

  /opt/AutoDock-Vina

  # ADFR Suite

  /opt/adfr

  # miniconda

  /opt/conda

  ```



## MGLTools



**Notice: MGLTools image is working well on macOS, it havn't been tested on other platforms. It may not be able to work directly on Linux, for more info, please [check](https://stackoverflow.com/questions/48546124/what-is-linux-equivalent-of-host-docker-internal).**



* Setup [XQuartz](https://www.xquartz.org/)



* Enable GLX



  ```bash

  # Run in Terminal

  defaults write org.macosforge.xquartz.X11 enable_iglx -bool true

  ```



* Add localhost into access control list (Run every time you restart your computer)



  ```bash

  # Run in Terminal

  xhost +localhost

  ```



* Mount $PWD to /data and Run MGLTools



  ```bash

  docker run --rm -it -v $PWD:/data -v /tmp/.X11-unix:/tmp/.X11-unix ghcr.io/metaphorme/mgltools

  ```



**Notice: If the window of AutoDockTools disappeared, open XQuartz -> Windows -> AutoDockTools to turn it up.**



## Contribute



Contributions welcome! Please open an issue to discuess at first, fork this repository and submit a pull request.



## Credits



* [AutoDock Vina](https://vina.scripps.edu/)



* [ADFR suite](https://ccsb.scripps.edu/adfr/)



* [Meeko](https://github.com/forlilab/Meeko/blob/develop/LICENSE)



* [AutoDockTools (MGLTools)](https://github.com/users/Metaphorme/packages/container/package/mgltools)



* [P3TERX/Actions-OpenWrt](https://github.com/P3TERX/Actions-OpenWrt)



* [Mac OSX Catalinaに導入したDocker上でAutoDock Toolsを動かす](https://itsuka-naritai.com/2020/10/27/mac-osx-catalina%e3%81%ab%e5%b0%8e%e5%85%a5%e3%81%97%e3%81%9fdocker%e4%b8%8a%e3%81%a7autodock-tools%e3%82%92%e5%8b%95%e3%81%8b%e3%81%99/)



## License



* [AutoDock Vina](https://autodock-vina.readthedocs.io/en/latest/citations.html)



* [ADFR suite Non-Commercial Use](https://ccsb.scripps.edu/adfr/license/)



* [Meeko](https://github.com/forlilab/Meeko/blob/develop/LICENSE)



* [Metaphorme/AutoDock-Vina-Docker](https://github.com/Metaphorme/AutoDock-Vina-Docker/blob/main/LICENSE)



  ```

  MIT License

  

  Copyright (c) 2022 Diazepam

  

  Permission is hereby granted, free of charge, to any person obtaining a copy

  of this software and associated documentation files (the "Software"), to deal

  in the Software without restriction, including without limitation the rights

  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

  copies of the Software, and to permit persons to whom the Software is

  furnished to do so, subject to the following conditions:

  

  The above copyright notice and this permission notice shall be included in all

  copies or substantial portions of the Software.

  

  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

  SOFTWARE.

  ```